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haitsubi
2024-03-19
> hw3ss24 <- readSPSS("C:/Users/haitsubi/Desktop/hw3ss24.sav", rownames=FALSE, stringsAsFactors=TRUE, tolower=FALSE)
> hw3ss24 <- readSPSS("C:/Users/haitsubi/Desktop/hw3ss24.sav", rownames=FALSE, stringsAsFactors=TRUE, tolower=FALSE)
> library(lme4)
> null_model_reml <- lmer(f1txcomp ~ 1 + (1 | f1sch_id), data = hw3ss24, REML = TRUE)
> null_model_fiml <- update(null_model_reml, REML = FALSE)
> summary(null_model_reml)
Linear mixed model fit by REML ['lmerMod']
Formula: f1txcomp ~ 1 + (1 | f1sch_id)
Data: hw3ss24
REML criterion at convergence: 31379.3
Scaled residuals:
Min 1Q Median 3Q Max
-2.75601 -0.77554 -0.00053 0.76322 2.57383
Random effects:
Groups Name Variance Std.Dev.
f1sch_id (Intercept) 15.03 3.876
Residual 80.74 8.986
Number of obs: 4292, groups: f1sch_id, 253
Fixed effects:
Estimate Std. Error t value
(Intercept) 49.3308 0.2828 174.4
> summary(null_model_fiml)
Linear mixed model fit by maximum likelihood ['lmerMod']
Formula: f1txcomp ~ 1 + (1 | f1sch_id)
Data: hw3ss24
AIC BIC logLik deviance df.resid
31384.6 31403.7 -15689.3 31378.6 4289
Scaled residuals:
Min 1Q Median 3Q Max
-2.75556 -0.77537 -0.00017 0.76335 2.57326
Random effects:
Groups Name Variance Std.Dev.
f1sch_id (Intercept) 14.95 3.866
Residual 80.74 8.986
Number of obs: 4292, groups: f1sch_id, 253
Fixed effects:
Estimate Std. Error t value
(Intercept) 49.3309 0.2823 174.8
> model_f1ses <- lmer(f1txcomp ~ f1ses + (1 | f1sch_id), data = hw3ss24,REML = TRUE)
> model_f1locus2 <- lmer(f1txcomp ~ f1locus2 + (1 |f1sch_id), data = hw3ss24,REML = TRUE)
> model_f1cncpt2 <- lmer(f1txcomp ~ f1cncpt2 + (1 |f1sch_id), data = hw3ss24,REML = TRUE)
> summary(model_f1ses)
Linear mixed model fit by REML ['lmerMod']
Formula: f1txcomp ~ f1ses + (1 | f1sch_id)
Data: hw3ss24
REML criterion at convergence: 29782.3
Scaled residuals:
Min 1Q Median 3Q Max
-3.10792 -0.73493 0.01517 0.75169 2.83153
Random effects:
Groups Name Variance Std.Dev.
f1sch_id (Intercept) 6.099 2.470
Residual 72.738 8.529
Number of obs: 4150, groups: f1sch_id, 253
Fixed effects:
Estimate Std. Error t value
(Intercept) 50.1591 0.2088 240.18
f1ses 4.8508 0.1908 25.42
Correlation of Fixed Effects:
(Intr)
f1ses 0.127
> summary(model_f1locus2)
Linear mixed model fit by REML ['lmerMod']
Formula: f1txcomp ~ f1locus2 + (1 | f1sch_id)
Data: hw3ss24
REML criterion at convergence: 30137
Scaled residuals:
Min 1Q Median 3Q Max
-2.95525 -0.74811 -0.01519 0.74979 3.04522
Random effects:
Groups Name Variance Std.Dev.
f1sch_id (Intercept) 12.55 3.542
Residual 72.64 8.523
Number of obs: 4184, groups: f1sch_id, 253
Fixed effects:
Estimate Std. Error t value
(Intercept) 49.6465 0.2624 189.20
f1locus2 4.5704 0.2129 21.47
Correlation of Fixed Effects:
(Intr)
f1locus2 0.031
> summary(model_f1cncpt2)
Linear mixed model fit by REML ['lmerMod']
Formula: f1txcomp ~ f1cncpt2 + (1 | f1sch_id)
Data: hw3ss24
REML criterion at convergence: 30487.4
Scaled residuals:
Min 1Q Median 3Q Max
-2.63700 -0.76643 0.00297 0.76786 2.61824
Random effects:
Groups Name Variance Std.Dev.
f1sch_id (Intercept) 14.34 3.787
Residual 78.38 8.853
Number of obs: 4187, groups: f1sch_id, 253
Fixed effects:
Estimate Std. Error t value
(Intercept) 49.5112 0.2783 177.94
f1cncpt2 2.1806 0.2084 10.46
Correlation of Fixed Effects:
(Intr)
f1cncpt2 0.015
> final_model_Hox2_reml <- lmer(f1txcomp ~ f1ses + f1locus2 + f1cncpt2 + (1 | f1sch_id), data = hw3ss24, REML = TRUE)
> summary(final_model_Hox2_reml)
Linear mixed model fit by REML ['lmerMod']
Formula: f1txcomp ~ f1ses + f1locus2 + f1cncpt2 + (1 | f1sch_id)
Data: hw3ss24
REML criterion at convergence: 28694.5
Scaled residuals:
Min 1Q Median 3Q Max
-3.3614 -0.7236 0.0049 0.7271 3.2545
Random effects:
Groups Name Variance Std.Dev.
f1sch_id (Intercept) 5.604 2.367
Residual 66.339 8.145
Number of obs: 4050, groups: f1sch_id, 253
Fixed effects:
Estimate Std. Error t value
(Intercept) 50.3056 0.2011 250.167
f1ses 4.3288 0.1871 23.137
f1locus2 4.0820 0.2503 16.308
f1cncpt2 -0.1821 0.2324 -0.784
Correlation of Fixed Effects:
(Intr) f1ses f1lcs2
f1ses 0.117
f1locus2 0.009 -0.139
f1cncpt2 0.002 0.023 -0.547
> final_model_Hox2_fiml <- lmer(f1txcomp ~ f1ses + f1locus2 + f1cncpt2 + (1 | f1sch_id), data = hw3ss24)
> summary(final_model_Hox2_fiml)
Linear mixed model fit by REML ['lmerMod']
Formula: f1txcomp ~ f1ses + f1locus2 + f1cncpt2 + (1 | f1sch_id)
Data: hw3ss24
REML criterion at convergence: 28694.5
Scaled residuals:
Min 1Q Median 3Q Max
-3.3614 -0.7236 0.0049 0.7271 3.2545
Random effects:
Groups Name Variance Std.Dev.
f1sch_id (Intercept) 5.604 2.367
Residual 66.339 8.145
Number of obs: 4050, groups: f1sch_id, 253
Fixed effects:
Estimate Std. Error t value
(Intercept) 50.3056 0.2011 250.167
f1ses 4.3288 0.1871 23.137
f1locus2 4.0820 0.2503 16.308
f1cncpt2 -0.1821 0.2324 -0.784
Correlation of Fixed Effects:
(Intr) f1ses f1lcs2
f1ses 0.117
f1locus2 0.009 -0.139
f1cncpt2 0.002 0.023 -0.547
> model_Hox3_feses_1 <- lmer(f1txcomp ~ f1ses + f1locus2 + f1cncpt2 + f1ses_1 +(1 | f1sch_id), data = hw3ss24, REML
+ = TRUE)
> model_Hox3_tchcomm <- lmer(f1txcomp ~ f1ses + f1locus2 + f1cncpt2 + tchcomm +(1 | f1sch_id), data = hw3ss24, REML
+ = TRUE)
> summary(model_Hox3_feses_1)
Linear mixed model fit by REML ['lmerMod']
Formula: f1txcomp ~ f1ses + f1locus2 + f1cncpt2 + f1ses_1 + (1 | f1sch_id)
Data: hw3ss24
REML criterion at convergence: 28660.1
Scaled residuals:
Min 1Q Median 3Q Max
-3.4245 -0.7202 0.0090 0.7279 3.3117
Random effects:
Groups Name Variance Std.Dev.
f1sch_id (Intercept) 4.533 2.129
Residual 66.259 8.140
Number of obs: 4050, groups: f1sch_id, 253
Fixed effects:
Estimate Std. Error t value
(Intercept) 50.6436 0.1974 256.512
f1ses 3.8740 0.2032 19.062
f1locus2 4.0663 0.2496 16.289
f1cncpt2 -0.1653 0.2316 -0.714
f1ses_1 2.8686 0.4802 5.973
Correlation of Fixed Effects:
(Intr) f1ses f1lcs2 f1cnc2
f1ses -0.006
f1locus2 0.005 -0.122
f1cncpt2 0.007 0.015 -0.547
f1ses_1 0.275 -0.411 -0.014 0.016
> summary(model_Hox3_tchcomm)
Linear mixed model fit by REML ['lmerMod']
Formula: f1txcomp ~ f1ses + f1locus2 + f1cncpt2 + tchcomm + (1 | f1sch_id)
Data: hw3ss24
REML criterion at convergence: 28697.5
Scaled residuals:
Min 1Q Median 3Q Max
-3.3686 -0.7208 0.0065 0.7274 3.2623
Random effects:
Groups Name Variance Std.Dev.
f1sch_id (Intercept) 5.629 2.373
Residual 66.316 8.143
Number of obs: 4050, groups: f1sch_id, 253
Fixed effects:
Estimate Std. Error t value
(Intercept) 50.46295 0.23520 214.555
f1ses 4.30898 0.18767 22.961
f1locus2 4.07999 0.25028 16.302
f1cncpt2 -0.18299 0.23233 -0.788
tchcomm 0.04936 0.03806 1.297
Correlation of Fixed Effects:
(Intr) f1ses f1lcs2 f1cnc2
f1ses 0.060
f1locus2 0.005 -0.138
f1cncpt2 0.000 0.023 -0.547
tchcomm 0.517 -0.077 -0.006 -0.003
> Hox_model3_reml <- lmer(f1txcomp ~ f1ses + f1locus2 + f1cncpt2 + f1ses_1 +(1 | f1sch_id), data = hw3ss24, REML =
+ TRUE)
> Hox_model3_fiml <- lmer(f1txcomp ~ f1ses + f1locus2 + f1cncpt2 + f1ses_1 +(1 | f1sch_id), data = hw3ss24)
> summary(Hox_model3_reml)
Linear mixed model fit by REML ['lmerMod']
Formula: f1txcomp ~ f1ses + f1locus2 + f1cncpt2 + f1ses_1 + (1 | f1sch_id)
Data: hw3ss24
REML criterion at convergence: 28660.1
Scaled residuals:
Min 1Q Median 3Q Max
-3.4245 -0.7202 0.0090 0.7279 3.3117
Random effects:
Groups Name Variance Std.Dev.
f1sch_id (Intercept) 4.533 2.129
Residual 66.259 8.140
Number of obs: 4050, groups: f1sch_id, 253
Fixed effects:
Estimate Std. Error t value
(Intercept) 50.6436 0.1974 256.512
f1ses 3.8740 0.2032 19.062
f1locus2 4.0663 0.2496 16.289
f1cncpt2 -0.1653 0.2316 -0.714
f1ses_1 2.8686 0.4802 5.973
Correlation of Fixed Effects:
(Intr) f1ses f1lcs2 f1cnc2
f1ses -0.006
f1locus2 0.005 -0.122
f1cncpt2 0.007 0.015 -0.547
f1ses_1 0.275 -0.411 -0.014 0.016
> summary(Hox_model3_fiml)
Linear mixed model fit by REML ['lmerMod']
Formula: f1txcomp ~ f1ses + f1locus2 + f1cncpt2 + f1ses_1 + (1 | f1sch_id)
Data: hw3ss24
REML criterion at convergence: 28660.1
Scaled residuals:
Min 1Q Median 3Q Max
-3.4245 -0.7202 0.0090 0.7279 3.3117
Random effects:
Groups Name Variance Std.Dev.
f1sch_id (Intercept) 4.533 2.129
Residual 66.259 8.140
Number of obs: 4050, groups: f1sch_id, 253
Fixed effects:
Estimate Std. Error t value
(Intercept) 50.6436 0.1974 256.512
f1ses 3.8740 0.2032 19.062
f1locus2 4.0663 0.2496 16.289
f1cncpt2 -0.1653 0.2316 -0.714
f1ses_1 2.8686 0.4802 5.973
Correlation of Fixed Effects:
(Intr) f1ses f1lcs2 f1cnc2
f1ses -0.006
f1locus2 0.005 -0.122
f1cncpt2 0.007 0.015 -0.547
f1ses_1 0.275 -0.411 -0.014 0.016
> Hox_model4_reml <-lmer (f1txcomp ~ f1ses +f1locus2 +f1cncpt2+f1ses_1+(1 |f1sch_id ), data = hw3ss24, REML = TRUE)
> Hox_model4_fiml <-lmer (f1txcomp ~ f1ses +f1locus2 +f1cncpt2+tchcomm +(1 |f1sch_id ), data = hw3ss24, REML = TRUE)
> summary(Hox_model4_reml)
Linear mixed model fit by REML ['lmerMod']
Formula: f1txcomp ~ f1ses + f1locus2 + f1cncpt2 + f1ses_1 + (1 | f1sch_id)
Data: hw3ss24
REML criterion at convergence: 28660.1
Scaled residuals:
Min 1Q Median 3Q Max
-3.4245 -0.7202 0.0090 0.7279 3.3117
Random effects:
Groups Name Variance Std.Dev.
f1sch_id (Intercept) 4.533 2.129
Residual 66.259 8.140
Number of obs: 4050, groups: f1sch_id, 253
Fixed effects:
Estimate Std. Error t value
(Intercept) 50.6436 0.1974 256.512
f1ses 3.8740 0.2032 19.062
f1locus2 4.0663 0.2496 16.289
f1cncpt2 -0.1653 0.2316 -0.714
f1ses_1 2.8686 0.4802 5.973
Correlation of Fixed Effects:
(Intr) f1ses f1lcs2 f1cnc2
f1ses -0.006
f1locus2 0.005 -0.122
f1cncpt2 0.007 0.015 -0.547
f1ses_1 0.275 -0.411 -0.014 0.016
> summary(Hox_model4_fiml)
Linear mixed model fit by REML ['lmerMod']
Formula: f1txcomp ~ f1ses + f1locus2 + f1cncpt2 + tchcomm + (1 | f1sch_id)
Data: hw3ss24
REML criterion at convergence: 28697.5
Scaled residuals:
Min 1Q Median 3Q Max
-3.3686 -0.7208 0.0065 0.7274 3.2623
Random effects:
Groups Name Variance Std.Dev.
f1sch_id (Intercept) 5.629 2.373
Residual 66.316 8.143
Number of obs: 4050, groups: f1sch_id, 253
Fixed effects:
Estimate Std. Error t value
(Intercept) 50.46295 0.23520 214.555
f1ses 4.30898 0.18767 22.961
f1locus2 4.07999 0.25028 16.302
f1cncpt2 -0.18299 0.23233 -0.788
tchcomm 0.04936 0.03806 1.297
Correlation of Fixed Effects:
(Intr) f1ses f1lcs2 f1cnc2
f1ses 0.060
f1locus2 0.005 -0.138
f1cncpt2 0.000 0.023 -0.547
tchcomm 0.517 -0.077 -0.006 -0.003
> final_Hox_model4_reml<-lmer (f1txcomp ~ f1ses +f1locus2 +f1cncpt2+f1ses_1+tchcomm + (1 |f1sch_id ), data = hw3ss24,
+ REML = TRUE)
> final_Hox_model4_fiml<-lmer (f1txcomp ~ f1ses +f1locus2 +f1cncpt2+f1ses_1+tchcomm + (1 |f1sch_id ), data = hw3ss24,
+ REML = FALSE)
> summary(final_Hox_model4_reml)
Linear mixed model fit by REML ['lmerMod']
Formula: f1txcomp ~ f1ses + f1locus2 + f1cncpt2 + f1ses_1 + tchcomm + (1 | f1sch_id)
Data: hw3ss24
REML criterion at convergence: 28664.8
Scaled residuals:
Min 1Q Median 3Q Max
-3.4253 -0.7200 0.0094 0.7295 3.3123
Random effects:
Groups Name Variance Std.Dev.
f1sch_id (Intercept) 4.573 2.139
Residual 66.256 8.140
Number of obs: 4050, groups: f1sch_id, 253
Fixed effects:
Estimate Std. Error t value
(Intercept) 50.666823 0.224698 225.488
f1ses 3.874146 0.203232 19.063
f1locus2 4.065979 0.249661 16.286
f1cncpt2 -0.165490 0.231674 -0.714
f1ses_1 2.848678 0.489462 5.820
tchcomm 0.008087 0.036581 0.221
Correlation of Fixed Effects:
(Intr) f1ses f1lcs2 f1cnc2 f1ss_1
f1ses -0.004
f1locus2 0.003 -0.122
f1cncpt2 0.003 0.015 -0.547
f1ses_1 0.151 -0.404 -0.013 0.017
tchcomm 0.474 0.002 -0.004 -0.007 -0.184
> summary(final_Hox_model4_fiml)
Linear mixed model fit by maximum likelihood ['lmerMod']
Formula: f1txcomp ~ f1ses + f1locus2 + f1cncpt2 + f1ses_1 + tchcomm + (1 | f1sch_id)
Data: hw3ss24
AIC BIC logLik deviance df.resid
28671.0 28721.4 -14327.5 28655.0 4042
Scaled residuals:
Min 1Q Median 3Q Max
-3.4265 -0.7211 0.0087 0.7315 3.3148
Random effects:
Groups Name Variance Std.Dev.
f1sch_id (Intercept) 4.465 2.113
Residual 66.206 8.137
Number of obs: 4050, groups: f1sch_id, 253
Fixed effects:
Estimate Std. Error t value
(Intercept) 50.66720 0.22325 226.954
f1ses 3.87401 0.20315 19.069
f1locus2 4.06641 0.24951 16.298
f1cncpt2 -0.16589 0.23152 -0.717
f1ses_1 2.84916 0.48681 5.853
tchcomm 0.00796 0.03634 0.219
Correlation of Fixed Effects:
(Intr) f1ses f1lcs2 f1cnc2 f1ss_1
f1ses -0.004
f1locus2 0.003 -0.122
f1cncpt2 0.003 0.015 -0.547
f1ses_1 0.151 -0.406 -0.013 0.017
tchcomm 0.474 0.002 -0.004 -0.007 -0.183